To determine a genome wide function in chromatin remodeling, we employed micrococcal nuclease (MNase)-seq analysis. We used cell lines that were conditionally deleted of Lsh through inducible cre-recombinase expression or lost Lsh through proteolytic degradation by using an auxin-inducible degron system. We found that Lsh protects MNase accessibility at transcriptional regulatory regions characterized by DNase I hypersensitivity and certain histone 3 (H3) tail modifications associated with enhancers. Lsh mediated changes in nucleosome occupancy are independent of DNA methylation level and are characterized by reduced H3 occupancy. While Lsh mediated nucleosome occupancy prevents binding sites for transcription factors in wild type cells, depletion of Lsh leads to an increase in binding of ectopically expressed tissue specific transcription factors to their respective binding sites. Our data suggests that Lsh mediated chromatin remodeling can modulate nucleosome positioning at a subset of putative enhancers. This in turn contributes to the preservation of cellular identity through regulation of transcription factor binding. Our data suggest that Lsh mediated changes of nucleosome density are a primary consequence of Lsh function and DNA methylation changes are subsequent events. We identified a specific role for Lsh in guarding and preserving chromatin structure to prevent access to tissue specific enhancers or regulatory regions. Revealing Lsh molecular function on chromatin provides insights in the pathophysiology of the ICF syndrome.